For these, use a Custom Reference Genome (and Build, as needed). Below is how. The first is a summary, the second more detailed.

Be sure to quickly review formatting on the second link in the section Troubleshooting to avoid problems. Specifically, use chromosome names that are unique, simple alphanumeric with optional underscores, and do not contain description content. Meaning, only this: ">identifier" - (without quotes) - nothing after, no whitespace (spaces, tabs), no additional text content.